Hi Antonin,

Thanks a lot for your reply.

Somehow, in the link you sent, I could not find any response to your email. But I can see your email to Anderson and command line parameters.

As I am not an expert in using FreeSurfer, so would it be possible for you to share detailed step-by-step guide and PALM command after I run mri_glmfit command and how and where to include '?h.white.avg.area.mgh' file?

I would really appreciate any help.

On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Martin,

I think yes, you can use PALM with FreeSurfer surfaces, see my conversation with Anderson on FSL list:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088

but beware not to forget to include average the vertex area (?h.white.avg.area.mgh) file.

Antonin

If you don't have an orthogonal design, then you can't use 
mri_glmfit-sim. I think you can use PALM:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

I have not tried it yet.

Anderson, can you use PALM with surfaces?






On 03/06/2017 05:23 PM, Martin Juneja wrote:
> Hi Dr. Greve,
>
> I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 
> 1000 3 permcsd --sim-sign abs --cwpvalthresh .05
> It gives error that ERROR: design matrix is not orthogonal, cannot be 
> used with permutation.
>
> But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 
> 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it works.
>
> I am not sure whether I will have to make the design matrix 
> orthogonal. If so, could you please tell me how that can be done?
>
> Or using --perm-force should be fine?
>
> Thanks.
>
> On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>     This is a problem with using LGI in that it is already extremely
>     smooth
>     that the smoothness exceeds the limit of the look up table that we
>     supply. I  recommend that you not use a gaussian-based correction for
>     LGI. Instead, use permutation (see mri_glmfit-sim --help).
>
>
>
>     On 03/06/2017 01:36 PM, Martin Juneja wrote:
>     > Hello everyone,
>     >
>     > I am trying to extract clusters showing significant correlation
>     > between LGI and a behavioral measure. I am able to extract PCC and
>     > sig.mgh but at the last step when I try to run simulation command to
>     > view corrected results and I run:
>     >
>     > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05
>     > --2spaces
>     >
>     > I get following error:
>     >
>     > ERROR: cannot find
>     >
>     
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>     >
>     > But I can see mc-z.csd file in fwhm30 etc.
>     >
>     > Full message on terminal window is attached following.
>     >
>     > Any help would be really appreciated.
>     >
>     > ----- Full message ----
>     >
>     > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd
>     dods --C
>     > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
>     lh.MEQ_LGI.glmdir
>     >
>     > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>     >
>     > SURFACE: fsaverage lh
>     >
>     > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
>     >
>     > /usr/local/freesurfer/bin/mri_glmfit-sim
>     >
>     > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
>     >
>     > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
>     >
>     > Mon Mar  6 11:11:13 MST 2017
>     >
>     > setenv SUBJECTS_DIR
>     > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
>     >
>     > FREESURFER_HOME /usr/local/freesurfer
>     >
>     > Original mri_glmfit command line:
>     >
>     > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd
>     dods --C
>     > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
>     lh.MEQ_LGI.glmdir
>     >
>     > DoSim = 0
>     >
>     > UseCache = 1
>     >
>     > DoPoll = 0
>     >
>     > DoPBSubmit = 0
>     >
>     > DoBackground = 0
>     >
>     > DiagCluster = 0
>     >
>     > gd2mtx = dods
>     >
>     > fwhm = 35.073391
>     >
>     > ERROR: cannot find
>     >
>     
> /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
>     >
>     >

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